The Letter
by Ellex
Summary: McKay receives bad news far too late, and Caldwell's suspicions lead him to jump to conclusions. Slight spoilers for 'Siege 3'. Now COMPLETE with alternate ending.
1. Chapter 1

Title: The Letter

Pairing: could be McShep…there's not enough to this to know for sure

Feedback: Please

Disclaimer: Stargate: Atlantis is not owned by me, nor do I make any material profit from this story.

Spoilers: for S2 'Siege 3', sort of

Warnings: Heavy angst. Tears.

A/N: My genre dial is kind of stuck on angst at the moment, much as I'd like to write something amusing...I've had this lurking at the back of my brain for a while, though.

OOOOOOOOOOOOOOO

The meeting had run overtime, as so many of them did, despite the fact that they no longer had the horrible urgency of the 'no power/no supplies/no weapons/Wraith heading straight for them' situation they'd lived with for far too long defining every thought, word, and deed. At least they seemed to have accomplished something, since every issue on Elizabeth's lengthening list had been discussed and some plan of action conceived for each and every one. Rodney was tired, but it was the good kind of tired, the kind where he felt he could go back to his quarters and maybe take a little nap, just to refresh his brain, and not wake up shaking and sweating from a nightmare fifteen minutes after falling asleep.

He shut down his laptop, tucked it under his arm, and had nearly reached the door when Caldwell called out to him.

"Doctor McKay, I nearly forgot - I have a letter for you." The commander of the Daedalus pulled a sealed envelope from his pocket and handed it to the scientist, who accepted it wordlessly.

Rodney headed for the door again, tearing the letter open and scanning the paper inside. As he read, his face suddenly drained of color and he staggered. The paper fell from suddenly numb fingers.

Sheppard, who was nearest, saw the look on his face and lunged to catch him before his knees gave way, lowering Rodney gently to the floor as he gasped for breath. Carson knelt at his side, efficiently checking vitals while calling for help from the infirmary.

Elizabeth picked up the letter. "Oh my god," she whispered after she'd read the terse, impersonal contents. "Rodney, I'm so sorry."

Rodney didn't hear her - he was staring blankly at John while tears rolled unnoticed down his cheeks.

"No, please, oh, no, no, no..." he moaned.

John wordlessly gathered the scientist in his arms and Rodney broke down completely. Harsh, painful sobs, eerily silent, shook his body. Carson placed a comforting hand on Rodney's back, looking up at Elizabeth for an explanation.

Caldwell looked on with surprise and a certain amount of distaste.

"His sister died," she told them quietly. "Several months ago, it seems. Her husband and two children, as well...a car accident. The Air Force was unable to deliver the video message he sent to her."

fin


	2. Chapter 2

A/N: I had no idea there was more to this story, and I have no idea how much more there may be. I'm just as surprised as you.

* * *

John didn't look up, didn't say anything, just shifted position to hold Rodney tighter. Carson exchanged a look with him and radioed the infirmary, canceling the EMT's. Another look, between the physician and Elizabeth, carried so much unspoken dialogue that Caldwell felt, for a moment, that he'd gone deaf.

"I'm very sorry for your loss, Doctor McKay," he said stiffly. The scientist didn't seem to hear him, still weeping raggedly onto Sheppard's shoulder. As he watched, the soldier began to rub McKay's back in long strokes, smoothing out the wrinkled shirt.

Caldwell cleared his throat abruptly. "Lieutenant Colonel, I'm sure Doctor Beckett can handle this. I have some concerns I'd like to discuss with you before the Daedalus sets off for Earth again."

He wasn't prepared for Beckett's sudden glare of undisguised outrage, for Sheppard to ignore him completely, or for Elizabeth's hand on his arm, surprisingly firm, pulling him away. His astonishment lasted long enough for her to drag him out of the conference room, closing the doors behind them.

"Let's leave them alone for a bit, Colonel." Her voice was hard and cold. She stalked toward her office, glancing back only once to make sure he was following.

The moment the door of her office closed, she turned on him. "I'm sorry if Doctor McKay's reaction to the news of his sister's death or the comfort offered by his friends makes you uncomfortable, Colonel, but I will not permit you to disrupt his grief with minor administrative issues. Rodney now has no family left on Earth. He's going to need the support of his family here on Atlantis, all the support we can give him."

"Look, Doctor Weir," Caldwell jumped in, "I support 'Don't ask, don't tell'. What Sheppard and McKay do in private, off duty, is their business and not something I can control, whether I think it's detrimental to their team or not. But that kind of public display of affection is completely inappropriate, and it's going to get them in trouble. I can't pretend not to have seen it. I'll let it go this time, out of deference to Doctor McKay's loss, but it can't happen again."

Elizabeth's eyes had gone wide. "You think – that John and Rodney…" She walked around the desk and sat down heavily, leaning her elbows on the desktop and putting her head in her hands.

"Colonel…do you have much experience with the Gate teams at the SGC? I know your qualifications to command the Daedalus, your experiences in various hot spots on Earth. I know you've been through Earth's Stargate on missions. But have you seen the kind of friendship, the deep rapport that Gate teams develop? SG-1's exploits are legendary among those who have the security clearance to read their mission reports. They've defied death again and again, triumphed over impossible odds, experienced things most people can't even imagine. The affection between them is unmistakable, and to the best of my knowledge, none of them have had physical relations with each other."

She raised her head and gazed straight at him, her sharp eyes searching his.

"Here on Atlantis, we were cut off from Earth for the better part of a year. Just a few hundred people, living in each others pockets, under constant threat from an adversary that could drain the very life from us with a touch. We've had to rely on each other, without any backup, no supplies or equipment except what we brought with us, what we could trade for, what we found and could make work in Atlantis, in the knowledge that every day could be our last.

"We can't go home at the end of the day, Colonel. Leave time is spent in the same place we work, with the same people we work with. Friendships here reach the same intensity as romantic relationships, without any sexual aspect necessary. If you find yourself that uncomfortable with seeing a man offering comfort to a grieving friend, if you're that ready to jump to unwarranted conclusions…you might want to consider resigning command of the Daedalus. Because there's nothing physical between Rodney and myself, either, and I would prefer to be in there with him, holding him, rather than disabusing you of your unfounded suspicions."

"But you're – "

"A woman? I'm also in command of Atlantis, Colonel. It would be inappropriate for me to get involved with the head of my science department. Nevertheless, Rodney is my friend, and as such, no one on Atlantis – none of the original personnel – would consider it inappropriate or suspicious if I were to hold Rodney the same way John is holding him now. And none of them, seeing John comforting Rodney, would entertain the notions you have."


	3. Chapter 3

A/N: I seem to have left the angst behind. I tell you, I don't write these stories- they write me.

* * *

The next morning, Caldwell was astonished to see McKay show up at his office door, looking tired and pale and oddly more mature in jeans and a T-shirt. 

"I, um…I wanted to apologize for that…scene yesterday. I don't usually…that is, the, ah, news was – well, unexpected. I don't have any other…family left." His hands, usually so active when he spoke, were tightly clasped, and he couldn't meet Caldwell's eyes. "It's – I'm mortified to have…well…"

"Don't worry about it, Doctor McKay," Caldwell answered, eager to halt the speech that was becoming painfully embarrassing to both of them. "Doctor Weir explained to me that you've been under a great deal of stress lately. I'm sorry I wasn't able to prepare you for the bad news, but I was unaware of the contents of the letter."

"Oh, no, it – it wasn't your fault. I just – I tried to contact her, you know? When we were on Earth. Now I know why she didn't get back to me." His gaze dropped to the floor, his mouth turning down sharply at the corners, and for one hugely awkward moment, Caldwell thought he might start crying again.

Sheppard's unruly head appeared around the door, a pleased grin lighting his face at the sight of McKay. "Oh, hey, there you are! I was looking for you. Hello, sir," he added to Caldwell, almost as an afterthought. The rest of his body followed him into the room, and Caldwell couldn't help but stare. The sleeveless, knee-length black and red wetsuit left little to the imagination, and fit Sheppard perfectly.

"You're not dressed, Rodney. We've got to get going if we want to catch the waves." He slung a casual arm over McKay's shoulders. "Elizabeth gave us a couple of days off, said we're all too stressed out, so I'm taking Rodney to the mainland. There are some great beaches there, I thought I'd teach him to surf."

"I'm not going to allow you to drown me in the name of cheering me up. I agreed to go, but I intend to sit on the sand and catch up on the latest scientific journals from Earth. I'm sure I'll get horribly sunburned, but there's no way I'm putting on a wetsuit, and we have no idea what might be in the water. The marine biologists are still studying the chemical composition of the _water_, for heaven's sake." His tone was sharp and irritated, but McKay's face had brightened noticeably.

"That's why we're going to be _on top_ of the water, Rodney." Sheppard leaned nonchalantly against the scientist. "That's the whole point of surfing. No more excuses, Elizabeth told me to get you out in the sunshine and fresh air. Are you done with the Colonel?"

"I'm out in the sunshine and fresh air all the time! Every time we go on a mission, it's nothing but fresh air. Trees, and bugs, and fresh air. And rocks. And more trees. And – "

Caldwell jumped in, eager to get them out of his office. Sheppard was laying the 'buddy' thing on a bit thick, and he could see McKay lapping it up eagerly. He'd heard them at it before, lobbing quips and complaints back and forth like verbal tennis…or like flirting.

"Yes, Colonel, we're done here. Doctor McKay was just leaving."

He knew he sounded a little terse, but he had a sneaking suspicion that Doctor Weir had spoken to Sheppard after her angry lecture to him yesterday, and now Sheppard was taunting him with his suspicions. He wouldn't put it past Sheppard to do so whether he and McKay were in a relationship or not, which further clouded the issue. This was exactly why Caldwell had been unhappy with Weir's insistence on Sheppard maintaining military command of Atlantis. He had the loyalty of his men, certainly, and the support of the full science contingent, not just McKay, which was even more impressive for a career screw-up who had a history of arguing with and disobeying superior officers. But his casual manner and easygoing style of command set a bad example, invited disobedience and laziness, and this – this _thing _he had going with McKay was completely inappropriate and against military regs. It was understandable when they had been completely cut off from Earth, with little to no hope of ever contacting home, but Sheppard should have broken it off as soon as regular contact with Earth was restored.

Caldwell watched the two men leave, Sheppard's arm still around McKay's shoulders, and came to a decision. He had to know. He _needed_ to know if his suspicions were correct. This could be the issue that ousted Sheppard from command of Atlantis, and was just one more reason he _should _be removed.

Among the original expedition, there was one person who had repeatedly made it clear that Weir, Sheppard and McKay did not have his unquestioning loyalty. One person whom Caldwell could be sure wouldn't lie to him.

He checked his laptop for the location of the lab occupied by one Doctor Calvin Kavanagh.

* * *

The video sent to Earth via a microburst communication through the wormhole had given Caldwell the impression of a pinch-faced, pedantic man with even fewer social graces than McKay. The reality only confirmed his assessment. The ridiculous affectation of the pony-tail only compounded the offensiveness of his manner. He looked and sounded like he smelled something disgusting, and suspected the odor originated with whomever he was speaking to. 

Caldwell had thought Kavanagh would jump eagerly to his aid, particularly given his video diatribe against the Atlantis triumvirate and his litany of procedures abandoned, dangers ignored, and reckless chances taken. But the man listened quietly and spent a long moment in serious thought before replying.

"I have to tell you that I'm rather surprised to be asked something like this, especially by you, of all people. I'd like to know if you're conducting an official investigation, because this does rather violate the 'don't ask, don't tell' rule."

"It's not an official investigation yet. But I can't ignore the circumstantial evidence, not when Sheppard keeps flaunting it in front of me. I'd hoped I could rely on your support and previous experience with Colonel Sheppard and Doctor McKay."

Kavanagh's smile was unmistakably cold. "Circumstantial evidence is not grounds for investigation, Colonel Caldwell. I will, however, tell you what I know to be fact."

He felt a righteous thrill at the assertion of solid evidence, and leaned forward eagerly. He had made the right decision in coming to talk to Kavanagh. Sheppard's time on Atlantis was limited, as of this moment.

* * *

A/N: I'm so mean...I know what Kavanagh is going to tell Caldwell, but you'll just have to wait until I write it down. 

And I'd just like to say thanks so much to everyone who has read and reviewed this, and any of my other stories. I keep meaning to acknowledge you all, and I get so caught up in the process of writing that I forget. I see many of the same names again and again, and I feel like I have my own little fan club. You have all been so sweet and so complimentary, I'm in terrible danger of getting a swelled ego. I really appreciate your kind words, and I promise - updating my stories is _never_ dependent on reviews. As long as I keep getting ideas, I'll keep writing and posting. :-x


	4. Chapter 4

A/n: Thank you all so much for reviewing, for following this story, for your patience while I try to figure out what happens next! I love reading your speculations about it. I sincerely hope to be able to add to this story every day.

Warning for mention of homosexuality. Nothing explicit.

* * *

"Rumor," Kavanagh began, "would have it that Doctor McKay and Lieutenant Colonel Sheppard are going at it like bunnies every chance they get. In their quarters, on the balconies, in the Puddle Jumpers, on the mainland, in Doctor Weir's office…but I'm sure you get the picture.

"There's no consensus on when they started. Few put it any earlier than before the hurricane, and some date it as late as just after you showed up. Most believe Sheppard to have been the instigator, but say that McKay developed feelings of attraction first. Majority opinion also holds that at least one, if not both, are bisexual rather than exclusively homosexual."

He pushed his glasses up his nose, looking thoughtful while Caldwell squirmed inwardly, impatient to get to the facts. He found Kavanagh's pretentious, lecturing tone incredibly irritating, but couldn't afford to offend him.

"I haven't heard a single person who was a member of our original expedition express any dissatisfaction with or prejudice against them. Intriguing, don't you think? Of course, there are those who believe that it is Doctor McKay and Doctor Beckett who are involved with each other, and a fair number who feel there is some kind of romantic attachment between Sheppard and Doctor Weir."

He paused, frowning. "You know, I occasionally wonder if I should have studied psychology rather than concentrating on the hard sciences. I find collecting these rumors and speculations to be a highly entertaining pastime. There would certainly be less personal risk involved, although there would also be fewer tangible results."

At this point, Caldwell couldn't help but interrupt. "I'm not interested in gossip and innuendo, Doctor. I'm looking for evidence, and you told me you had it."

Kavanagh was silent, his small eyes gazing speculatively at Caldwell. "I didn't say I had evidence," he finally replied. "I said I would tell you what I knew to be fact. The fact is that there _is_ no evidence, or at least if anyone has any, they aren't telling. The fact is that, while I'm not familiar with Colonel Sheppard's schedule, I see a good deal more of McKay than I would like, and although I don't care for him personally, I can't fault his work ethic. If he manages even half the number of assignations with Sheppard that are credited to them, he must have more energy and stamina than any three Marines put together."

A sardonic smile settled on his smooth face. "I may not approve of Doctor Weir's policies , or Colonel Sheppard's laissez-faire style of command, or McKay's 'smarter-than-thou' attitude, but I will not compromise my own ethics just to remove any of them from their positions. Your eagerness to begin a witch-hunt, in defiance of United States military regulations and based on nothing more than hearsay and your own prejudices, does not recommend you to me as a capable replacement." Acid dripped from his voice as he finished bitterly, "I may be a jerk, Colonel Caldwell, but I'm an honest jerk."


	5. Chapter 5

A/N: I opened my e-mail earlier this evening. 31 messages, and almost every one was about this story! That's a record for me. I still hope to post a section each day, even though I still have no idea where this is going. Thanks so much to everyone who has read and/or reviewed. I love reading what you think, and using that to go in a completely different direction. grin

* * *

Caldwell rose to his feet, fists clenched, glaring at Kavanagh. The temptation to punch the man was almost overwhelming.

Kavanagh, in turn, stood up, revealing himself to be several inches taller than the soldier. He loomed over Caldwell with all the natural menace of a former schoolyard bully.

"Would you like to know the latest rumors, Colonel? They involve Doctor Weir and yourself," he said calmly.

Surprise quenched Caldwell's anger quickly. He had been flirting mildly with Weir, mainly as a tactic to put her off her guard and see how far he could charm her, but he thought he'd been subtle about it. Or perhaps the rumor mill here on Atlantis was simply starved for new gossip and possible romance was seen everywhere, regardless of evidence or likelihood.

He forced himself to be calm, thanked Kavanagh for his time with stiff politeness, and left quickly. He would have to revise his plan. The Daedalus was scheduled to leave the next day, so he didn't have much time.

He needed to back off, approach the situation dispassionately, from a soldier's viewpoint. He'd become too involved, too eager to find evidence and get Sheppard out of his way. There had to be a vulnerability somewhere that he could exploit, just one person who knew something. And someone had to know something. It just wasn't possible to keep an affair a secret; not in a small, enclosed society like Atlantis, not between two people so much in the public eye as Sheppard and McKay. But the people closest to them, the people who would know, were all ridiculously, blindly loyal to them. He would have to resort to intimidation to learn what he wanted to know.

He ran down a mental list of candidates in his mind, quickly realizing that his best bet was probably with the scientific community. The military people would be either implacably loyal to Sheppard or cling to the 'don't ask, don't tell' rule. The scientists, however, were bound by no such rule, and McKay had a reputation for antagonizing even those who liked him. There was, however, no way to tell who might be willing to talk, or who might have solid evidence.

Inspiration hit him like a bullet from a .357 Magnum. There were really only two people, in all of Atlantis, who would know, beyond all doubt, what Sheppard and McKay were doing to each other. One of them had already proven himself impossible to intimidate. The other…well, McKay had shown himself to be a competent man in a crisis, but he'd seen the fear in his eyes, on his face. Every emotion, every thought, showed plain as day on that face, and Caldwell would have instant confirmation of his suspicions as soon he confronted McKay. He had little doubt that McKay could be either physically intimidated, or threatened with the recall of his precious Lieutenant Colonel back to Earth for an investigation. Better yet, he could approach the scientist as a friend, concerned for Sheppard's career, and induce him to spill everything without any hint of duress.


	6. Chapter 6

"Thank you for coming, Doctor McKay," Caldwell waved him to take the chair on the other side of his desk. "I appreciate your taking time out of your busy schedule to see me."

"I wanted to see the latest modifications Hermiod made to the drive system, anyway. I can't imagine what could be so important that you wanted to see me here, though."

Caldwell schooled his face not to reflect his delight at having McKay in his own private office on the Daedalus. "I'm concerned about Colonel Sheppard. His career could be in grave danger. There's even a possibility that he could be recalled to Earth and face a court martial."

McKay stared at him in surprise. "Court martial? Sheppard? But – he hasn't done anything wrong! He's – don't tell him I said so, but he's the best thing that could have happened to the expedition. I've worked for the US military for years, and he's the best officer I've ever dealt with."

Caldwell smiled. "Your loyalty is admirable, Doctor McKay, and Sheppard's record here in the Pegasus Galaxy speaks for itself, but there are certain things that simply can't be overlooked. I've come to you because I believe you have his best interests at heart." He leaned back to deliver the coup de grace. "I know about you and Colonel Sheppard. I know what you've been doing – together."

"Me and Colonel – " McKay's face registered momentary incomprehension before guilt blossomed across it. "You mean – you know about – "

He was right. The man's face showed _everything_, and any doubt he'd had was now put to rest. "Yes, Doctor McKay, I know. And so do my superiors back on Earth. I've pleaded on Sheppard's behalf, but I'm not sure how much it will help." This was perfect. McKay was completely taken in by his show of altruistic concern.

"I just can't believe...it's harmless, you know? Neither of us would do anything to endanger Atlantis. I just – I needed…" McKay looked down at his hands, clenched in his lap.

"I understand, Doctor. A man has certain needs, desires, that can't always be met in the ordinary way. Living here in another galaxy for so long out of contact with Earth must have made it even harder. Look, Doctor McKay," he leaned forward, deliberately creating the impression of imparting a confidence, "I think I can salvage the situation. I don't think you should tell Colonel Sheppard about our conversation. I'm afraid he might decide to try and bluff his way out of this, or even resign his commission, and it's far too late for that. I think it would be better if you wrote out a full confession for me to take back to Earth, along with a promise that you'll cease all illicit activities. As a civilian, you can't be prosecuted, and I might be able to persuade the investigating panel that you were the instigator. That Sheppard was just trying to help you."

McKay nodded slowly. "I, um…I'll do that. I'll have it ready before your departure." He rose unsteadily, not looking at Caldwell, looking slightly dazed. At the door, he turned back.

"Are you sure that's the best thing to do? There's no chance of, you know," he waved his hand in air vaguely, "plausible deniability, or something like that?"

Caldwell shook his head solemnly. "I'm afraid not, Doctor McKay. The best you can hope for now is to minimize the damage, and the only person who can do that is you."

* * *

A/N: Wasn't that a surprise? Just as much for me as it was for you, I can honestly say. Now, you may _think_ that this chapter has turned the story into slash…but read again, and you'll see that nothing has really been confirmed. Is Rodney talking about the same thing as Caldwell, or has the Colonel been a little too vague in his accusation?

I'm sorry to leave you hanging like this, but I promise that I don't know any more than you do. Hopefully I'll figure it out by tomorrow. Thanks so much to everyone who has read and reviewed this. I'm astonished and gratified at the overwhelming response I've received.


	7. Chapter 7

A.N: Please don't be upset with me about this chapter. I don't know what came over me. I promise you'll learn what Sheppard and McKay have been up to in Part 8.

* * *

Caldwell waited…and waited…and waited, but nothing from McKay arrived by the end of the day. Departure of the Daedalus for Earth was scheduled for the following morning, at 0900 Atlantis time, which didn't leave much leeway. He debated with himself over dinner as to whether he should approach McKay again or remain patient. His biggest worry was that the scientist would tell Sheppard or Weir about their conversation. If that happened, Caldwell was sunk. He had taken things much too far, mentioning an investigative panel. 

His sleep that night was restless and filled with images of Sheppard smirking at him, McKay making awkward and suggestive innuendoes about Caldwell's own sexuality. The worst was a surreal dream in which Elizabeth Weir informed him, while hugging a sobbing McKay, that Sheppard was dead and it was Caldwell's fault, and that McKay was threatening to blow up the Daedalus if Caldwell didn't publicly confess his guilt in full view of all personnel on Atlantis.

The nightmare left him sweating and shaking, and feeling oddly ashamed of himself. He had to admit that his actions had been less than admirable or professional, and in the face of no concrete evidence he had told lies to a man still vulnerable and grieving over the loss of the only family he had. His obsession had even led him to put himself in an extremely precarious position that might threaten his career.

He thought about losing command of the Daedalus. He liked commanding the ship, liked the personnel and the daily routine. It was nice to be back on Earth every few months, nice to be on the move. He'd never liked sitting still, and after only a week on Atlantis found himself ready to set off again. If he commanded Atlantis, he'd have to deal with Air Force, Marines, and civilians, who comprised over half the population of the city. He didn't particularly care for the civilians; although there was a small contingent of non-military scientists on the Daedalus, the vast majority of its crew were military. He would be able to lead missions through the Stargate, but after reading the mission reports, it seemed like it consisted of a great deal of trudging through various landscapes and waiting around while the scientists did their thing.

What he liked was commanding, delegating, organizing, making plans and decisions and seeing them carried out. He wanted command of Atlantis for the prestige of it, and because Sheppard's – how had Kavanagh put it? – 'laissez-faire style' made him itch to take charge. But the very fact that Sheppard had the loyalty of so many people, both military and civilian, showed that his method was effective. He'd seen some minor issues involving integrating the new arrivals into the existing population, difficulties Sheppard seemed to solve with a smile and smart-ass remark, but nothing that he could point to as a major problem. The man rubbed Caldwell the wrong way, had made some poor decisions along the way, ran a command so loose and informal he couldn't figure out how anyone knew what they were supposed to do – but it worked. It had worked for the year Atlantis had been cut off from Earth, and it continued to work, no matter how much Caldwell disliked it.

And while any affair between McKay and Sheppard was indeed against military regulations, the whole 'don't ask, don't tell' situation was so delicate that there was no telling quite how Air Force brass would react to his accusation. Add to that the fact that this was all taking place in another galaxy on a hugely top secret, joint military/civilian, multi-national expedition…any such aberrations in personal relationships might well be deliberately overlooked, and Caldwell himself might come out smelling rather distinctly of sour grapes.

By the time he rose and dressed for breakfast, Stephen Caldwell had made his decision. He would search out McKay and tell him to forget their conversation. He would say the situation was not nearly as bad as he had painted it, and that he just wanted to make sure McKay understood how serious it could be.

When he found the scientist, McKay was in Weir's office, waving his hands frantically as he spoke. Judging by the look on Elizabeth's face, easily visible through the transparent walls, he was in a great deal of trouble, and Caldwell broke into a cold sweat as he realized just how much trouble he, too, might be in.


	8. Chapter 8

Before Caldwell could retreat, Weir had spotted him through the transparent walls of her office and gestured for him to enter.

"Did you know about this, Colonel?" she asked furiously.

McKay answered before Caldwell could even figure out what to say. "No, he doesn't know anything, Elizabeth. It's entirely my fault. It was my idea, I made Sheppard do it. I know it's against all the rules, and it's probably immoral, and…I needed…I don't know…something to make me feel less impotent. After I learned about my sister…I just wanted to do something that would make me feel good."

"I hope it did feel good, Rodney, because I, for one, am appalled and disgusted. And I don't believe for a moment that Colonel Sheppard is in any way innocent. I wouldn't be at all surprised if it was really his idea." She cut off McKay's protest with a glare. "No, I don't want to hear another word. I'll decide what to do about this when I've calmed down. In the meantime, consider yourself confined to quarters, Rodney. Don't even think about contacting Sheppard first, I want to speak to him before you've had a chance to get your stories straight. You're dismissed."

McKay's shoulders drooped as he left, giving Caldwell a pained grimace. He turned back to Elizabeth to see her collapse into her chair and put her hands over her face.

"You did know, didn't you?" she asked quietly. "Don't bother to deny it, Rodney already gave you away. He told me he couldn't bluff to save his life, and he was right. I still don't know how he took Kolya in."

It seemed the cat was out of the bag now, but judging by Weir's reaction to McKay's confession, it appeared that her previous liberal views went out the window when confronted by reality. Perhaps the situation could be salvaged after all.

"I suspected," he told her. "Enough to speak to McKay and advise him to come clean, hoping to at least give him and Sheppard a chance. I'm not sure how they'll react to this back on Earth, though. Sheppard, at least, might find himself in a lot of trouble."

She raised her head to stare at him. "I'd have thought you knew – Colonel, this idea was brought up while we were on Earth. I mentioned it to Colonel Sheppard and Doctor McKay only as a possible last-ditch attempt if it looked like the Wraith intended to strip every planet in the Pegasus Galaxy. Giving away nuclear bombs is _not_ my idea of good trade relations. I had no idea that Rodney would decide to go ahead and manufacture several bombs and put them aside for the future. He and Sheppard have given away three of them to people we have trade agreements with."

It was Caldwell's turn to stare. "He gave away…" It took a few minutes for him to regain his composure. Clearing his throat, he finally said, "Yes, I did know about the plan to give weapons to natives of this galaxy as a last resort against the Wraith, but I didn't know McKay was giving away nuclear devices. Please tell me it wasn't to people like the Genii who might be able to reverse engineer our designs."

"No," she sighed, "he said the casings are sealed and the people he gave them to aren't advanced enough to figure out the technology even if they get them open. No real damage has been done, fortunately. I'd appreciate it if you'd be willing to keep this to yourself. I seriously doubt it would be enough to get Sheppard into any serious trouble, but it certainly doesn't look good that they did this without permission and right under my nose. I think the only reason this happened is because Rodney was so upset about his sister, he needed to do something he felt was constructive."

Caldwell sat lost in thought for a moment. Perhaps this was for the best. He'd had second thoughts about persecuting Sheppard and McKay anyways. He could have found himself in a very bad position, should McKay have realized what he'd been trying to get the scientist to confess.

"I don't see why this has to go any further," he told her. "I'm willing to forget this conversation ever happened. You know McKay better than I do; if you say he won't do it again, I believe you. Now," he smiled at her, "it's time I and my ship were on their way back to Earth. I'll see you in a few months, Elizabeth."

She returned his smile warmly. "Have a safe trip, Stephen," she replied.

He passed Sheppard and McKay on his way through the GateRoom, whispering furiously at each other. Sheppard caught Caldwell's eye as he passed, and winked broadly. McKay turned to see, and a sardonic grin spread across his face. He could feel their eyes on him until the doors closed behind him, and he made his way gratefully back to his own command.

fin

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A/N: Virtual chocolates go to Dr. Dredd, who figured out what John and Rodney were up to even before I did.

I was tempted to give this a tragic ending, to tie in with the tragic beginning…but I just couldn't disappoint everyone. You got lucky – I like happy endings.


	9. Chapter 9

The alternate, tragic, slash ending. I just _had_ to write it. Original rating still applies. Warning for character death.

* * *

McKay didn't stop talking when Caldwell entered Weir's office.

"I swear, Elizabeth, it was only a few times, we aren't – there's nothing going on now. It was just – just stress relief, you know? Just two guys helping each other out, letting off a little steam. I didn't tell you because there's nothing to tell. There's no reason for any investigation, no reason for John – for Sheppard to be punished." McKay was wringing his hands, his voice shaking. He turned frantically to Caldwell.

"You said you'd help. You'll put in a good word for him, explain that he was just doing it to help me? Sheppard isn't gay, you can't – you can't accuse him of that. It isn't fair. You can't let them ruin his career because of me."

Elizabeth turned a stern gaze on Caldwell. "You didn't tell me there was an investigation going on. I don't appreciate being left in the dark and made to look like a fool. You should have come to me first, Colonel."

He thought furiously, stalling for time by clearing his throat. "I did, Doctor Weir, and you shut me down. You insisted that Doctor McKay and Colonel Sheppard were not involved in any kind of inappropriate relationship. But the facts proved otherwise, and I felt my only recourse was to confront Doctor McKay. I'm trying to help them, Elizabeth, not condemn them."

"This is all my fault," McKay moaned, sitting down abruptly. "I didn't know you hadn't told Elizabeth about this, you should have said. I just wanted to let her know that I was taking full responsibility for everything. Here," he snatched a CD off Weir's desk and handed it to Caldwell, "my confession. And my personal guarantee that it will never happen again."

"Will that be enough, Colonel?" Elizabeth asked. "I'd hate to see this become an issue, and believe me, it could be very bad for everyone. There are too many civilians and military personnel on Atlantis from countries that don't have such restrictive and discriminatory policies about homosexuality for any kind of disciplinary action concerning it not to cause a great deal of unrest and upset."

"I certainly hope so, but I can't guarantee anything. If Sheppard is relieved of command, I'll do my best to make sure the reason why doesn't become popularly known. We do try to be discreet about these things." Inside, Caldwell was exultant, but he carefully preserved the mask of friendly concern.

* * *

Shortly afterward, as he stowed his gear in his quarters on the Daedalus, he carefully locked McKay's precious confession in his desk. Command of Atlantis was as good as his, or at least, not in Sheppard's reckless hands any longer. Success had wiped away all his doubts like they had never existed. McKay would be upset for while, certainly, but Caldwell had no doubt that he could handle the scientist's uncertain temperament. Hadn't he skillfully manipulated the man into giving away himself and his lover, while having no proof at all?

He slipped the key to the desk into the hole, and felt a sudden, intense pain travel from his fingers, up his arm, and into his chest, leaving a trail of freezing cold behind it. His legs folded beneath him and every muscle seemed to spasm at once, leaving him sprawled on the floor. Unable to move, even to blink or breathe, he couldn't feel his fingers or his toes, then his hands and feet, numbness creeping up farther and farther until he felt he was just a consciousness gazing out of blurred eyes. He didn't feel the lack of air in his lungs or the slowing beat of his heart.

A shape moved into the fixed field of his vision, and he heard a voice whispering in his ear.

"It's a neat little device, don't you think? Works instantly. Unfortunately, the records left by the Ancients indicate that it has no effect on the Wraith, even though it works perfectly on humans. Absolutely undetectable, too. Completely paralyzes you while leaving you awake and aware, then triggers a neat little brain aneurysm. Makes you wonder just what the Ancients really intended it for. It serves my purposes, though, because it gets you out of the way without any suspicion of murder."

He couldn't make out the face in front of him as his eyes dried out and his vision faded into blank whiteness, but the high, sharp voice was unmistakable.

"I can't let you do it. I can't let you take him away from me, do you understand? My parents are dead, my sister is gone…I need him, Colonel, and he needs me. I can't believe you actually thought I'd fall for it. There is no investigation, is there? You started this all on your own. You have no evidence except my confession. Elizabeth will keep her mouth shut, the last thing she wants is someone else in charge of the military on Atlantis.

"Did you forget that I'm a genius? Go up against me, Colonel, and you'll lose. In fact, you've already lost. In a moment, you'll be dead, I'll remove the device I planted in your desk and my confession, and no one will have any idea that your death wasn't completely natural. Such a tragedy, but those aneurysms are almost impossible to detect, aren't they? I've already programmed the security cameras so they won't record me moving around on the Daedalus, and if I meet up with anyone, well…I'm supposed to be here, aren't I? One last check on the drive systems before takeoff.

"John Sheppard is _mine_, Colonel. Nothing is going to change that, and no one is ever going to take him away from me." His hearing was fading now, too, along with the last remnants of conscious thought, but the low chuckle was still audible. "You lose, Caldwell. Everyone who goes up against me loses, sooner or later. And you lost the moment you delivered that letter."

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A/N: Okay, this really _is_ the end. Hope you had as much fun as I did, and thanks so much for all the lovely reviews and feedback. Words can't express how much I appreciate you all. 


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